The defiant southern region of Okinawa countersued Japan's government Friday over local resistance to a new US military base, the latest chapter in deepening mistrust between central authorities and the strategic island.

The lawsuit by Okinawa prefecture comes after the central government sued it last month amid a long-running drama between Tokyo, keen to satisfy security ally the United States, and Okinawa, where frustration over a seven-decade American military presence is rife.

Pacifist sentiments run high on the island that accounts for less than one percent of Japan's total land area but hosts about 75 percent of US military facilities in the country.

Okinawa governor Takeshi Onaga renewed his pledge to prevent the central government from constructing a US Marine air base in the remote Henoko part of the island to replace the existing Futenma facility in a heavily populated area, widely seen as a potential danger to residents.

"We will resort to every possible measure and will not allow the new base to be built in Henoko," he told a press conference.

In October, Onaga cancelled a 2013 approval for the project by his predecessor, saying it was not legally sound, prompting Tokyo to seek court action.

Okinawa's suit, filed in the prefectural capital of Naha, asks the court to revive his cancellation order of a landfill permit, which is currently nullified by the central government, court and local officials said.

Chief Cabinet Secretary Yoshihide Suga described the latest legal action as "extremely regrettable," insisting the initial approval was legal and formed a precedent that allows landfill work to continue.

Defence Minister Gen Nakatani said that the government would carry on with construction despite the lawsuit.

"We are doing this work in order to remove the danger of the Futenma air station as well as concerns of local residents as soon as possible," he told reporters.

Work in the Henoko district of Nago city in the island's north is only in the initial stages, with crews setting up sea floats and a makeshift bridge necessary for the landfill work.

Japan and the United States first proposed moving Futenma in 1996, though both insisted it must remain in Okinawa -- a key area from which US troops and aircraft can react to potential conflicts throughout Asia.

But residents have insisted Futenma should be closed and a replacement built elsewhere in another part of Japan or overseas, saying they can no longer live with the noise pollution, accidents and occasional crimes committed by US service members.